Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LNZN9

Calculation Name: 2OTP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OTP

Chain ID: A

ChEMBL ID:

UniProt ID: Q8N149

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1834232.067495
FMO2-HF: Nuclear repulsion 1758142.683262
FMO2-HF: Total energy -76089.384233
FMO2-MP2: Total energy -76311.721885


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-2.7790.9460.07-1.024-2.7710.001
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.027
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A5LYS10.9221.0383.810-0.9980.170-0.011-0.456-0.7020.002
4A6PRO0-0.017-0.0126.3730.5420.5420.0000.0000.0000.000
5A7THR00.0130.0078.9380.1500.1500.0000.0000.0000.000
6A8LEU0-0.017-0.01412.341-0.008-0.0080.0000.0000.0000.000
7A9TRP00.0540.00615.2860.0150.0150.0000.0000.0000.000
8A10ALA00.0210.00318.996-0.018-0.0180.0000.0000.0000.000
9A11GLU-1-0.898-0.95521.654-0.141-0.1410.0000.0000.0000.000
10A12PRO0-0.029-0.00723.5070.0110.0110.0000.0000.0000.000
11A13GLY00.0890.04026.1120.0120.0120.0000.0000.0000.000
12A14SER0-0.035-0.01524.748-0.014-0.0140.0000.0000.0000.000
13A15VAL00.0280.00526.379-0.004-0.0040.0000.0000.0000.000
14A16ILE0-0.0020.00928.2950.0070.0070.0000.0000.0000.000
15A17ILE00.0240.00731.6370.0020.0020.0000.0000.0000.000
16A18GLN00.0540.01934.313-0.007-0.0070.0000.0000.0000.000
17A19GLY0-0.0270.00334.4990.0050.0050.0000.0000.0000.000
18A20SER0-0.023-0.01832.7980.0060.0060.0000.0000.0000.000
19A21PRO0-0.022-0.00430.891-0.007-0.0070.0000.0000.0000.000
20A22VAL0-0.0160.00726.4160.0020.0020.0000.0000.0000.000
21A23THR00.008-0.00722.133-0.006-0.0060.0000.0000.0000.000
22A24LEU00.0250.02819.4180.0050.0050.0000.0000.0000.000
23A25ARG10.8930.95916.7770.1490.1490.0000.0000.0000.000
24A26CYS00.0740.05512.227-0.032-0.0320.0000.0000.0000.000
25A27GLN0-0.023-0.01712.2110.0290.0290.0000.0000.0000.000
26A28GLY00.042-0.0128.179-0.083-0.0830.0000.0000.0000.000
27A29SER0-0.0370.0084.6780.1430.232-0.001-0.006-0.0820.000
28A30LEU00.030-0.0116.796-0.049-0.0490.0000.0000.0000.000
29A31GLN0-0.067-0.0064.231-0.283-0.0470.000-0.019-0.2180.000
30A32ALA0-0.042-0.0277.427-0.135-0.1350.0000.0000.0000.000
31A33GLU-1-0.866-0.9438.888-0.322-0.3220.0000.0000.0000.000
32A34GLU-1-0.977-1.00510.484-0.473-0.4730.0000.0000.0000.000
33A35TYR0-0.058-0.03510.947-0.052-0.0520.0000.0000.0000.000
34A36HIS00.0260.02812.1050.0490.0490.0000.0000.0000.000
35A37LEU0-0.0050.02713.8470.0000.0000.0000.0000.0000.000
36A38TYR0-0.019-0.02516.778-0.022-0.0220.0000.0000.0000.000
37A39ARG10.9551.01117.8470.2180.2180.0000.0000.0000.000
38A40GLU-1-0.912-0.96520.062-0.144-0.1440.0000.0000.0000.000
39A41ASN0-0.007-0.02023.0310.0080.0080.0000.0000.0000.000
40A42LYS10.9640.99320.5020.1840.1840.0000.0000.0000.000
41A43SER00.1020.09520.069-0.019-0.0190.0000.0000.0000.000
42A44ALA00.0230.00620.8690.0060.0060.0000.0000.0000.000
43A45SER0-0.082-0.08116.472-0.008-0.0080.0000.0000.0000.000
44A46TRP0-0.0550.00619.0630.0160.0160.0000.0000.0000.000
45A47VAL00.0490.01215.381-0.029-0.0290.0000.0000.0000.000
46A48ARG10.8720.97116.7030.3120.3120.0000.0000.0000.000
47A49ARG10.9410.97015.6520.3440.3440.0000.0000.0000.000
48A50ILE0-0.080-0.03114.0750.0470.0470.0000.0000.0000.000
49A51GLN00.0460.01015.438-0.015-0.0150.0000.0000.0000.000
50A52GLU-1-0.862-0.90914.612-0.258-0.2580.0000.0000.0000.000
51A53PRO0-0.057-0.01915.6350.0340.0340.0000.0000.0000.000
52A54GLY00.0490.01515.249-0.015-0.0150.0000.0000.0000.000
53A55LYS10.8870.93016.6110.1580.1580.0000.0000.0000.000
54A56ASN00.0190.00213.703-0.046-0.0460.0000.0000.0000.000
55A57GLY00.0540.01414.9280.0270.0270.0000.0000.0000.000
56A58GLN0-0.080-0.05416.408-0.010-0.0100.0000.0000.0000.000
57A59PHE0-0.0030.00515.790-0.010-0.0100.0000.0000.0000.000
58A60PRO0-0.017-0.01821.2520.0060.0060.0000.0000.0000.000
59A61ILE00.0490.01624.954-0.007-0.0070.0000.0000.0000.000
60A62PRO0-0.0190.00027.8010.0070.0070.0000.0000.0000.000
61A63SER00.0580.01931.4110.0050.0050.0000.0000.0000.000
62A64ILE0-0.0390.00027.265-0.007-0.0070.0000.0000.0000.000
63A65THR0-0.023-0.09130.8640.0090.0090.0000.0000.0000.000
64A66TRP00.055-0.01431.323-0.004-0.0040.0000.0000.0000.000
65A67GLU-1-0.925-0.93529.257-0.130-0.1300.0000.0000.0000.000
66A68HIS00.0330.08326.975-0.002-0.0020.0000.0000.0000.000
67A69ALA00.0310.07926.114-0.014-0.0140.0000.0000.0000.000
68A70GLY00.0630.02824.6990.0040.0040.0000.0000.0000.000
69A71ARG10.9200.95818.2330.2160.2160.0000.0000.0000.000
70A72TYR0-0.122-0.11218.741-0.021-0.0210.0000.0000.0000.000
71A73HIS00.0400.01313.2250.0650.0650.0000.0000.0000.000
72A75GLN0-0.077-0.1057.7270.1890.1890.0000.0000.0000.000
73A76TYR0-0.045-0.0313.792-0.0930.3810.007-0.121-0.3590.000
74A77TYR0-0.0030.0186.626-0.417-0.4170.0000.0000.0000.000
75A78SER00.0160.0045.2580.1880.1880.0000.0000.0000.000
76A79HIS00.0260.0167.3980.0100.0100.0000.0000.0000.000
77A80ASN0-0.033-0.0167.9920.0800.0800.0000.0000.0000.000
78A81HIS0-0.0030.0083.576-1.139-0.4140.019-0.146-0.598-0.001
79A82SER00.0130.0085.5910.1630.1630.0000.0000.0000.000
80A83SER0-0.024-0.0083.046-1.105-0.4600.055-0.209-0.4910.000
81A84GLU-1-0.884-0.9353.5330.1440.5520.002-0.065-0.3450.000
82A85TYR0-0.052-0.0635.2580.1010.081-0.001-0.0020.0240.000
83A86SER00.033-0.0217.814-0.106-0.1060.0000.0000.0000.000
84A87ASP-1-0.939-0.95910.249-0.166-0.1660.0000.0000.0000.000
85A88PRO0-0.052-0.03413.538-0.022-0.0220.0000.0000.0000.000
86A89LEU0-0.0150.01416.4530.0350.0350.0000.0000.0000.000
87A90GLU-1-0.941-0.98119.222-0.106-0.1060.0000.0000.0000.000
88A91LEU0-0.051-0.00422.8240.0110.0110.0000.0000.0000.000
89A92VAL00.0230.00025.1050.0050.0050.0000.0000.0000.000
90A93VAL00.0030.02528.7260.0030.0030.0000.0000.0000.000
91A94THR0-0.031-0.02931.8950.0070.0070.0000.0000.0000.000
92A95GLY0-0.004-0.01235.184-0.001-0.0010.0000.0000.0000.000
93A96ALA0-0.0010.01037.1070.0000.0000.0000.0000.0000.000
94A97TYR00.010-0.00736.6180.0020.0020.0000.0000.0000.000
95A98SER0-0.013-0.01441.483-0.001-0.0010.0000.0000.0000.000
96A99LYS10.9440.98842.8830.0310.0310.0000.0000.0000.000
97A100PRO00.0660.01640.8640.0020.0020.0000.0000.0000.000
98A101THR0-0.091-0.03744.1810.0000.0000.0000.0000.0000.000
99A102LEU00.0190.02641.9170.0000.0000.0000.0000.0000.000
100A103SER0-0.016-0.02145.5170.0000.0000.0000.0000.0000.000
101A104ALA0-0.019-0.00547.8260.0010.0010.0000.0000.0000.000
102A105LEU0-0.0330.04148.5880.0000.0000.0000.0000.0000.000
103A106PRO00.005-0.01949.6200.0010.0010.0000.0000.0000.000
104A107SER0-0.007-0.06052.867-0.001-0.0010.0000.0000.0000.000
105A108PRO00.0240.00050.4050.0010.0010.0000.0000.0000.000
106A109VAL0-0.0120.01550.6240.0000.0000.0000.0000.0000.000
107A110VAL00.0510.04248.2640.0000.0000.0000.0000.0000.000
108A111THR00.0160.00551.3230.0000.0000.0000.0000.0000.000
109A112LEU0-0.002-0.01549.2680.0000.0000.0000.0000.0000.000
110A113GLY0-0.0150.00446.5440.0010.0010.0000.0000.0000.000
111A114GLY0-0.0070.01447.5850.0010.0010.0000.0000.0000.000
112A115ASN00.001-0.01146.5110.0010.0010.0000.0000.0000.000
113A116VAL00.000-0.00645.379-0.001-0.0010.0000.0000.0000.000
114A117THR0-0.042-0.01845.4190.0000.0000.0000.0000.0000.000
115A118LEU00.0130.00942.489-0.001-0.0010.0000.0000.0000.000
116A119GLN00.0270.01543.8130.0000.0000.0000.0000.0000.000
117A120CYS00.0130.00440.441-0.002-0.0020.0000.0000.0000.000
118A121VAL00.0160.00643.8960.0000.0000.0000.0000.0000.000
119A122SER00.0470.00044.316-0.002-0.0020.0000.0000.0000.000
120A123GLN0-0.0110.00346.3650.0000.0000.0000.0000.0000.000
121A124VAL0-0.020-0.00144.5820.0010.0010.0000.0000.0000.000
122A125ALA0-0.0150.00044.7020.0010.0010.0000.0000.0000.000
123A126PHE00.000-0.01839.590-0.003-0.0030.0000.0000.0000.000
124A127ASP-1-0.943-0.96437.221-0.035-0.0350.0000.0000.0000.000
125A128GLY00.0430.02035.603-0.001-0.0010.0000.0000.0000.000
126A129PHE0-0.072-0.03535.827-0.001-0.0010.0000.0000.0000.000
127A130ILE0-0.008-0.00532.072-0.001-0.0010.0000.0000.0000.000
128A131LEU00.0000.01635.0590.0020.0020.0000.0000.0000.000
129A132CYS0-0.079-0.06331.0600.0010.0010.0000.0000.0000.000
130A133LYS10.9280.95735.4780.0080.0080.0000.0000.0000.000
131A134GLU-1-0.854-0.93635.944-0.036-0.0360.0000.0000.0000.000
132A135GLY0-0.057-0.02436.1950.0040.0040.0000.0000.0000.000
133A136GLU-1-0.962-0.98536.547-0.006-0.0060.0000.0000.0000.000
134A137ASP-1-0.924-0.96134.283-0.016-0.0160.0000.0000.0000.000
135A138GLU-1-0.988-0.99229.613-0.032-0.0320.0000.0000.0000.000
136A139HIS00.0080.00332.0840.0010.0010.0000.0000.0000.000
137A140PRO0-0.035-0.01932.4630.0000.0000.0000.0000.0000.000
138A141GLN00.0060.03230.503-0.005-0.0050.0000.0000.0000.000
139A143LEU0-0.008-0.01730.2890.0000.0000.0000.0000.0000.000
140A144ASN0-0.010-0.02529.2140.0060.0060.0000.0000.0000.000
141A145SER0-0.049-0.01830.0280.0050.0050.0000.0000.0000.000
142A146HIS00.1090.06428.236-0.007-0.0070.0000.0000.0000.000
143A147SER00.032-0.01130.2400.0090.0090.0000.0000.0000.000
144A148HIS0-0.090-0.04425.036-0.007-0.0070.0000.0000.0000.000
145A149ALA00.0580.03429.1400.0050.0050.0000.0000.0000.000
146A150ARG10.9350.97029.1420.0200.0200.0000.0000.0000.000
147A151GLY0-0.014-0.00229.5480.0020.0020.0000.0000.0000.000
148A152TRP0-0.003-0.01730.0040.0030.0030.0000.0000.0000.000
149A153SER0-0.0090.01930.312-0.003-0.0030.0000.0000.0000.000
150A154TRP00.0620.00725.9340.0080.0080.0000.0000.0000.000
151A155ALA0-0.0140.01130.078-0.004-0.0040.0000.0000.0000.000
152A156ILE0-0.0310.00725.8400.0060.0060.0000.0000.0000.000
153A157PHE00.013-0.01527.741-0.004-0.0040.0000.0000.0000.000
154A158SER0-0.0040.00525.8100.0000.0000.0000.0000.0000.000
155A159VAL0-0.0040.00626.114-0.001-0.0010.0000.0000.0000.000
156A160GLY00.0110.01625.341-0.007-0.0070.0000.0000.0000.000
157A161PRO00.004-0.02825.8670.0070.0070.0000.0000.0000.000
158A162VAL0-0.0120.01625.2270.0060.0060.0000.0000.0000.000
159A163SER00.0610.03327.8810.0000.0000.0000.0000.0000.000
160A164PRO0-0.036-0.01428.1590.0030.0030.0000.0000.0000.000
161A165SER00.0510.01731.304-0.001-0.0010.0000.0000.0000.000
162A166ARG10.9280.95534.136-0.016-0.0160.0000.0000.0000.000
163A167ARG10.9540.97431.863-0.053-0.0530.0000.0000.0000.000
164A168TRP00.0510.03727.532-0.004-0.0040.0000.0000.0000.000
165A169SER0-0.016-0.00929.0460.0070.0070.0000.0000.0000.000
166A170TYR00.0100.01628.228-0.009-0.0090.0000.0000.0000.000
167A171ARG10.9290.96330.356-0.057-0.0570.0000.0000.0000.000
168A172CYS0-0.0130.00730.742-0.004-0.0040.0000.0000.0000.000
169A173TYR00.0420.00433.3040.0050.0050.0000.0000.0000.000
170A174ALA00.0200.00335.190-0.002-0.0020.0000.0000.0000.000
171A175TYR0-0.025-0.00837.1030.0010.0010.0000.0000.0000.000
172A176ASP-1-0.801-0.89239.5330.0130.0130.0000.0000.0000.000
173A177SER0-0.005-0.01542.138-0.001-0.0010.0000.0000.0000.000
174A178ASN0-0.062-0.02544.500-0.002-0.0020.0000.0000.0000.000
175A179SER0-0.042-0.07145.9010.0000.0000.0000.0000.0000.000
176A180PRO00.0410.06244.4510.0020.0020.0000.0000.0000.000
177A181TYR0-0.0100.00044.9230.0000.0000.0000.0000.0000.000
178A182VAL0-0.0270.00245.9100.0010.0010.0000.0000.0000.000
179A183TRP0-0.056-0.03640.7210.0010.0010.0000.0000.0000.000
180A184SER00.003-0.00237.4090.0000.0000.0000.0000.0000.000
181A185LEU0-0.014-0.01437.813-0.002-0.0020.0000.0000.0000.000
182A186PRO0-0.030-0.00235.9080.0010.0010.0000.0000.0000.000
183A187SER00.0250.00730.5220.0050.0050.0000.0000.0000.000
184A188ASP-1-0.941-0.98228.6150.1060.1060.0000.0000.0000.000
185A189LEU0-0.090-0.04228.768-0.002-0.0020.0000.0000.0000.000
186A190LEU00.0600.04423.3140.0100.0100.0000.0000.0000.000
187A191GLU-1-0.995-1.00625.6050.0790.0790.0000.0000.0000.000
188A192LEU0-0.016-0.00523.1150.0100.0100.0000.0000.0000.000
189A193LEU00.003-0.00218.8290.0030.0030.0000.0000.0000.000
190A194VAL00.0000.00021.199-0.011-0.0110.0000.0000.0000.000
191A195PRO0-0.0270.00419.1740.0120.0120.0000.0000.0000.000
192A196GLY00.0250.00821.715-0.014-0.0140.0000.0000.0000.000